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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#include <iostream> |
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|
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#include "io/RestWriter.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/simError.h" |
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#include "io/basic_teebuf.hpp" |
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|
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#include "brains/SnapshotManager.hpp" |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#define TAKE_THIS_TAG_INT 1 |
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#define TAKE_THIS_TAG_REAL 2 |
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#endif //is_mpi |
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#endif |
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|
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namespace oopse { |
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RestWriter::RestWriter(SimInfo* info) : |
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info_(info), outName_(info_->getRestFileName()) { |
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} |
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|
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RestWriter::~RestWriter() {} |
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|
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void RestWriter::writeZAngFile() { |
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std::ostream* zangStream; |
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|
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namespace OpenMD { |
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RestWriter::RestWriter(SimInfo* info, const std::string& filename, |
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std::vector<Restraint*> restraints ) : |
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info_(info){ |
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|
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//use master - slave mode, only master node writes to disk |
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif // is_mpi |
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if(worldRank == 0){ |
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#endif |
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|
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zangStream = new std::ofstream(outName_.c_str()); |
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output_.open(filename.c_str()); |
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|
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if(!output_){ |
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sprintf( painCave.errMsg, |
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"Could not open %s for restraint output.\n", |
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filename.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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output_ << "#time\t"; |
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|
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// TODO: get Restraint info from slave nodes: |
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std::vector<Restraint*>::const_iterator resti; |
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for(resti=restraints.begin(); resti != restraints.end(); ++resti){ |
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|
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if ((*resti)->getPrintRestraint()) { |
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std::string myName = (*resti)->getRestraintName(); |
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int myType = (*resti)->getRestraintType(); |
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|
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output_ << myName << ":"; |
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|
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if (myType & Restraint::rtDisplacement) |
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output_ << "\tPosition(angstroms)\tEnergy(kcal/mol)"; |
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|
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if (myType & Restraint::rtTwist) |
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output_ << "\tTwistAngle(radians)\tEnergy(kcal/mol)"; |
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|
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if (myType & Restraint::rtSwingX) |
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output_ << "\tSwingXAngle(radians)\tEnergy(kcal/mol)"; |
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|
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if (myType & Restraint::rtSwingY) |
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output_ << "\tSwingYAngle(radians)\tEnergy(kcal/mol)"; |
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|
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} |
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} |
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output_ << "\n"; |
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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|
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writeZangle(*zangStream); |
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|
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#endif |
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} |
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|
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RestWriter::~RestWriter() { |
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif // is_mpi |
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delete zangStream; |
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|
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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#endif |
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output_.close(); |
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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|
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#endif |
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} |
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|
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void RestWriter::writeZangle(std::ostream& finalOut){ |
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const int BUFFERSIZE = 2000; |
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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|
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Molecule* mol; |
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StuntDouble* integrableObject; |
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SimInfo::MoleculeIterator mi; |
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Molecule::IntegrableObjectIterator ii; |
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|
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#ifndef IS_MPI |
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// first we do output for the single processor version |
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finalOut |
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<< info_->getSnapshotManager()->getCurrentSnapshot()->getTime() |
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<< " : omega values at this time\n"; |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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|
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void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo){ |
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for (integrableObject = mol->beginIntegrableObject(ii); |
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integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(ii)) { |
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|
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sprintf( tempBuffer, |
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"%14.10lf\n", |
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integrableObject->getZangle()); |
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strcpy( writeLine, tempBuffer ); |
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finalOut << writeLine; |
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|
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} |
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} |
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|
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#else |
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int nproc; |
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MPI_Comm_size(MPI_COMM_WORLD, &nproc); |
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const int masterNode = 0; |
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|
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MPI_Status ierr; |
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int intObIndex; |
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int vecLength; |
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RealType zAngle; |
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std::vector<int> gIndex; |
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std::vector<RealType> zValues; |
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|
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if (worldRank == masterNode) { |
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std::map<int, RealType> zAngData; |
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for(int i = 0 ; i < nproc; ++i) { |
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if (i == masterNode) { |
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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|
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for (integrableObject = mol->beginIntegrableObject(ii); |
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integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(ii)) { |
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|
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intObIndex = integrableObject->getGlobalIntegrableObjectIndex(); |
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|
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zAngle = integrableObject->getZangle(); |
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zAngData.insert(std::pair<int, RealType>(intObIndex, zAngle)); |
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} |
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} |
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} else { |
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MPI_Recv(&vecLength, 1, MPI_INT, i, |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &ierr); |
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// make sure the vectors are the right size for the incoming data |
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gIndex.resize(vecLength); |
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zValues.resize(vecLength); |
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|
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MPI_Recv(&gIndex[0], vecLength, MPI_INT, i, |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &ierr); |
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MPI_Recv(&zValues[0], vecLength, MPI_REALTYPE, i, |
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TAKE_THIS_TAG_REAL, MPI_COMM_WORLD, &ierr); |
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|
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for (int k = 0; k < vecLength; k++){ |
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zAngData.insert(std::pair<int, RealType>(gIndex[k], zValues[k])); |
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} |
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gIndex.clear(); |
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zValues.clear(); |
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} |
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} |
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|
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finalOut << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() |
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<< " : omega values at this time\n"; |
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|
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std::map<int, RealType>::iterator l; |
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for (l = zAngData.begin(); l != zAngData.end(); ++l) { |
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|
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sprintf( tempBuffer, |
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"%14.10lf\n", |
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l->second); |
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strcpy( writeLine, tempBuffer ); |
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output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime(); |
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|
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finalOut << writeLine; |
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// output some information about the molecules |
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std::vector<std::map<int, Restraint::RealPair> >::const_iterator i; |
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std::map<int, Restraint::RealPair>::const_iterator j; |
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for( i = restInfo.begin(); i != restInfo.end(); ++i){ |
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for(j = (*i).begin(); j != (*i).end(); ++j){ |
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output_ << "\t" << (j->second).first << "\t" << (j->second).second; |
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} |
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|
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} else { |
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// pack up and send the appropriate info to the master node |
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for(int j = 1; j < nproc; ++j) { |
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if (worldRank == j) { |
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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|
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for (integrableObject = mol->beginIntegrableObject(ii); |
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integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(ii)) { |
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|
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// build a vector of the indicies |
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intObIndex = integrableObject->getGlobalIntegrableObjectIndex(); |
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gIndex.push_back(intObIndex); |
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|
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// build a vector of the zAngle values |
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zAngle = integrableObject->getZangle(); |
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zValues.push_back(zAngle); |
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|
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} |
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} |
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|
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// let's send these vectors to the master node so that it |
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// can sort them and write to the disk |
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vecLength = gIndex.size(); |
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|
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MPI_Send(&vecLength, 1, MPI_INT, masterNode, |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
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MPI_Send(&gIndex[0], vecLength, MPI_INT, masterNode, |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
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MPI_Send(&zValues[0], vecLength, MPI_REALTYPE, masterNode, |
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TAKE_THIS_TAG_REAL, MPI_COMM_WORLD); |
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|
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} |
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} |
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output_ << std::endl; |
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} |
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|
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#endif |
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} |
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|
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} |
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}// end namespace OpenMD |
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|
